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Bio::EnsEMBL::PaddedSlice Class Reference
Inheritance diagram for Bio::EnsEMBL::PaddedSlice:

List of all members.


Class Summary

Description

Used when dumping Slices which represet a portion of the sequence region
they map to e.g. the first section of human Y. The code will return N
as sequence if an attempt is made to retrieve sequence not covered by the
Slice given. This makes the code very memory efficient if sequence dumping
is carried out using subseq() calls.
 

Definition at line 14 of file PaddedSlice.pm.

Available Methods

protected Any __proxy ()
protected CodeRef __resolver ()
public void AUTOLOAD ()
public Code can ()
public void DESTROY ()
public Int end ()
public Boolean isa ()
public Int length ()
public Bio::EnsEMBL::PaddedSlice new ()
public Scalar seq ()
public Int start ()
public sub_Slice ()
public Scalar subseq ()

Method Documentation

protected Any Bio::EnsEMBL::Utils::Proxy::__proxy ( ) [inherited]
 
  Example			: -
  Description	: The proxy accessor
  Returntype 	: Any the proxied object
  Exceptions 	: None 
  Caller     	: -
  Status     	: -
 
Code:
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protected CodeRef Bio::EnsEMBL::PaddedSlice::__resolver ( )
  Description : Delegates all non-overriden actions onto the backing slice 
  Returntype  : CodeRef
  Exceptions  : None 
  Caller      : public
  Status      : -
 
Code:
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Reimplemented from Bio::EnsEMBL::Utils::Proxy.

public void Bio::EnsEMBL::Utils::Proxy::AUTOLOAD ( ) [inherited]
  Example     : -
  Description : Performs calls to __resolver() and installs the subroutine
                into the current package scope.
  Returntype  : None 
  Exceptions  : Thrown if __resolver() could not return a subroutine
  Caller      : -
  Status      : -
 
Code:
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public Code Bio::EnsEMBL::Utils::Proxy::can ( ) [inherited]
  Args       	: Method name to test
  Example			: $obj->can('__proxy');
  Description	: Overriden to provide can() support for proxies. Will return
                true if this object implements the given method or the
                proxied object can
  Returntype 	: Code; performs same as a normal can
  Exceptions 	: None
  Caller     	: caller
  Status     	: status
 
Code:
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public void Bio::EnsEMBL::Utils::Proxy::DESTROY ( ) [inherited]
  Example			: -
  Description	: Provided because of AutoLoad
  Returntype 	: None 
  Exceptions 	: None
  Caller     	: -
  Status     	: -
 
Code:
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public Int Bio::EnsEMBL::PaddedSlice::end ( )
  
  Example     : $slice->end();
  Description : Always returns the backing slice sequence region length
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -
 
Code:
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public Boolean Bio::EnsEMBL::Utils::Proxy::isa ( ) [inherited]
  Args        : Object type to test
  Example     : $obj->isa('Bio::EnsEMBL::Utils::Proxy');
  Description : Overriden to provide isa() support for proxies. Will return
                true if this object is assignable to the given type or the
                proxied object is
  Returntype  : Boolean; performs same as a normal can
  Exceptions  : None
  Caller      : caller
  Status      : status
 
Code:
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public Int Bio::EnsEMBL::PaddedSlice::length ( )
  
  Example     : $slice->length();
  Description : Delegates to end()
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -
 
Code:
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public Bio::EnsEMBL::PaddedSlice Bio::EnsEMBL::PaddedSlice::new ( )
  Arg [SLICE] : The Slice to proxy  
  Example     : my $newobj = Bio::EnsEMBL::PaddedSlice->new($myobj);
  Description : Provides a new instance of a padded slice
  Returntype  : Bio::EnsEMBL::PaddedSlice
  Exceptions  : None 
  Caller      : public
  Status      : -
 
Code:
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Reimplemented from Bio::EnsEMBL::Utils::Proxy.

public Scalar Bio::EnsEMBL::PaddedSlice::seq ( )
  
  Example     : my $seq = $slice->seq()
  Description : Returns the entire sequence of the backing slice but padded
                with N's at the beginning and the end of the slice where
                applicable
  Returntype  : Scalar string
  Exceptions  : None 
  Caller      : public
  Status      : -
 
Code:
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public Int Bio::EnsEMBL::PaddedSlice::start ( )
  Example     : $slice->start();
  Description : Always returns 1 since all padded slices start at 1
  Returntype  : Int
  Exceptions  : None 
  Caller      : public
  Status      : -
 
Code:
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public Bio::EnsEMBL::PaddedSlice::sub_Slice ( )

Undocumented method

Code:
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public Scalar Bio::EnsEMBL::PaddedSlice::subseq ( )
  
  Arg [1]     : Int; start position of the subslice
  Arg [2]     : Int; end position of the subslice
  Arg [3]     : Int; strand of the subslice  
  Example     : my $subseq = $slice->subseq(1, 1_000_000);
  Description : Returns a portion of the sequence padded with N's if required 
  Returntype  : Scalar string
  Exceptions  : None 
  Caller      : public
  Status      : -
 
Code:
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  Arg [1]     : Int; start position of the subslice
  Arg [2]     : Int; end position of the subslice
  Arg [3]     : Int; strand of the subslice  
  Example     : my $subseq = $slice->subseq(1, 1_000_000);
  Description : Returns a portion of the sequence padded with N's if required 
  Returntype  : Scalar string
  Exceptions  : None 
  Caller      : public
  Status      : -
 

/**


The documentation for this class was generated from the following file: